Affymetrix 10k, 100k and 500k Genotyping
Tell me about these three products
The Affymetrix GeneChip Human Mapping SNP arrays are a fast,
economic and powerful SNP-based genetic mapping tool.
The 10K single array product provides data on over 11,000 SNPs
distributed across the genome. The 100K set is comprised of a set
of two 50K arrays each with 50,000 SNPs and together, they provide
data on over 100,000 SNPs across the genome. The 500K Array set is
comprised of two 250K arrays, each capable of genotyping on average
250,000 SNPs. Please see below for a snapshot comparison of the
10K, 100K and 500K SNP coverage. In addition, you also have the
flexibility to choose to use single 50K or 250K arrays.
Figure 4:
We can offer contract research with all Affymetrix SNP genotyping
products.
A snapshot comparison of 10k, 100k, 500k SNP.
What are the advantages of using SNP array?
- The SNP density enables highly powered whole genome
studies.
- It allows you to stay in charge of your budgets. A complete
data set is generated from each DNA sample. This gives you the
flexibility to select those samples that will be the most
informative in your sample set. You can type them first, analyse
your genome wide data and then decide if you need to do more.
- The assay uses just 250ng of genomic DNA per chip - only as
much as is used up on just 50 microsatellites.
- Source BioScience LifeSciences has set up a high-throughput
mode of operation with multiple samples processed in parallel.
Typically, you will get data about 2 weeks after we start
processing.
How do I get started?
Using our experience and expertise from years of RNA expression
analysis on the Affymetrix platform, Source BioScience
LifeSciences will process your DNA samples efficiently, accurately
and economically (of course, we cannot guarantee that every project
will give a significant LOD score: this depends on mode of
inheritance, family structure and map location). We have kept costs
as low as possible with prices starting at about £400 per sample
(inclusive of chip, consumables and processing costs). Discounts
may be given for large projects. We offer free advice regarding
projects and data analysis. Contact us now to confirm pricing and
to get a custom proposal of work.
How should I supply my DNA?
The precise amount of DNA required for each sample will be a
minimum of 10ul at 50 ng /ul using reduced EDTA TE buffer (0.1 mM
EDTA, 10mM Tris HCl, pH8.0). Each array requires 250ng of DNA that
has preferably been tested by you for its integrity. If this is not
possible please send OD260/280 ratios of samples to confirm ratio
>1.8 for each sample. Samples may be accepted of a lower quality
at the discretion of Source BioScience LifeSciences but risk a
higher chance of poor quality PCR.
Sample IDs should be provided in Excel format. Samples to be
tested should be sent in a 96-well format on dry ice.
Contact us / telephone us to confirm your despatch arrangements
for samples. We strongly advise that samples are not posted on a
Thursday or Friday. Please post your samples to the following
address:
AffySNP,
Source BioScience
Units 24 and 25
William James House
Cowley Road
Cambridge CB4 0WU
United Kingdom
What if my samples don't pass the post PCR quality control
stage?
Samples that fail the PCR QC stage will be withdrawn from the
process at a cost of £100 per sample to cover consumable costs to
this point, unless instructed to continue at customers risk. We
would also offer customers the option of performing whole genome
amplification to "rescue" their samples. It is a very successful
method to obtain enough good quality DNA for further downstream
processing (more info).
When can you start my project?
We will only order chips and schedule your project on acceptance
of your personal quotation and receipt of the following
details:
- a signed copy of agreed quotation
- a signed copy of terms and conditions
- your details including purchase order with VAT exemption if it
applies.
We can only order chips and schedule your project on
receipt of these details.
When will I have to pay for the project?
For large projects you will be billed at the start of the
project for the Affymetrix GeneChip Mapping arrays since they need
to be ordered well in advance. You will be invoiced for the balance
upon completion of the project and delivery of results. You will be
notified in your proposal whether up-front payment for GeneChips is
required.
How will I receive the data?
Source BioScience LifeSciences will supply you with the data
from the samples on CD in strict confidence using Affymetrix
software in Excel format. For example:
|
SNP ID
|
TSC ID
|
dbSNP RS ID
|
Chr
|
Chr Location (deCODE map)
|
pp1 control 10xba 220503
|
Call 1
|
Call 2
|
Zone
|
|
SNP_A 1513509
|
tsc 111
|
rs 0713055
|
6
|
161960064
|
173.2
|
B
|
B
|
0.05
|
|
SNP_A 1513556
|
tsc 112
|
rs 0713056
|
6
|
161960122
|
173.2
|
A
|
A
|
0.53
|
|
SNP_A 1518411
|
tsc 256
|
rs 0949459
|
7
|
42288671
|
64.7
|
A
|
B
|
0.08
|
|
SNP_A 1511066
|
tsc 864
|
rs 0713298
|
10
|
67254514
|
83.4
|
A
|
A
|
0.21
|
This all looks great but I still would rather do
microsatellites
We continue to provide contract research using microsatellites
and have successfully completed more than 30 genome scans using
microsatellites.
I still have some questions, who can I speak to?
If you are interested in using the Affymetrix GeneChip Human
Mapping Arrays or have any queries please contact us with full
details of your study including the number of samples. We will
return a customised project proposal, and we can schedule your work
as soon as possible. Scheduling will only be arranged on receipt of
a valid purchase order number.